Umesh Varshney

Umesh Varshney

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Umesh Varshney

Publications by authors named "Umesh Varshney"

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88Publications

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Structural insights into the specificity and catalytic mechanism of mycobacterial nucleotide pool sanitizing enzyme MutT2.

J Struct Biol 2018 Oct 9. Epub 2018 Oct 9.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address:

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October 2018

Development of assay systems for amber codon decoding at the steps of initiation and elongation in mycobacteria.

J Bacteriol 2018 Sep 4. Epub 2018 Sep 4.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India

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September 2018

Sustenance of Escherichia coli on a single tRNAMet.

Nucleic Acids Res 2018 Sep 26. Epub 2018 Sep 26.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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September 2018

Antimicrobial activity of fusidic acid in Escherichia coli is dependent on the relative levels of ribosome recycling factor and elongation factor G.

FEMS Microbiol Lett 2018 Jul;365(13)

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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July 2018

Epidemiological, clinical and laboratory profile of scrub typhus cases detected by serology and RT-PCR in Kumaon, Uttarakhand: a hospital-based study.

Trop Doct 2018 Apr 24;48(2):103-106. Epub 2017 Nov 24.

6 Assistant Professor, Department of Microbiology, Government Medical College, Haldwani, Nainital, Uttarakhand, India.

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April 2018

Fidelity of translation in the presence of mammalian mitochondrial initiation factor 3.

Mitochondrion 2018 Mar 10;39:1-8. Epub 2017 Aug 10.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India. Electronic address:

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March 2018

Species-Specific Interactions of Arr with RplK Mediate Stringent Response in Bacteria.

J Bacteriol 2018 Mar 23;200(6). Epub 2018 Feb 23.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India

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March 2018

Distinct properties of a hypoxia specific paralog of single stranded DNA binding (SSB) protein in mycobacteria.

Tuberculosis (Edinb) 2018 01 3;108:16-25. Epub 2017 Oct 3.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advamced Scientific Research, Jakkur, Bangalore 560064, India. Electronic address:

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January 2018

Contributions of the N- and C-Terminal Domains of Initiation Factor 3 to Its Functions in the Fidelity of Initiation and Antiassociation of the Ribosomal Subunits.

J Bacteriol 2017 06 9;199(11). Epub 2017 May 9.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India

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June 2017

The IDL of E. coli SSB links ssDNA and protein binding by mediating protein-protein interactions.

Protein Sci 2017 02 26;26(2):227-241. Epub 2017 Jan 26.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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February 2017

Two highly conserved features of bacterial initiator tRNAs license them to pass through distinct checkpoints in translation initiation.

Nucleic Acids Res 2017 02;45(4):2040-2050

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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February 2017

Structure of the second Single Stranded DNA Binding protein (SSBb) from Mycobacterium smegmatis.

J Struct Biol 2016 12 19;196(3):448-454. Epub 2016 Sep 19.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India. Electronic address:

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December 2016

An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation.

Proc Natl Acad Sci U S A 2016 10 3;113(41):E6126-E6134. Epub 2016 Oct 3.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, India

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October 2016

The Termination Phase in Protein Synthesis is not Obligatorily Followed by the RRF/EF-G-Dependent Recycling Phase.

J Mol Biol 2016 09 31;428(18):3577-87. Epub 2016 May 31.

Max-Planck-Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité, Charitéplatz 1, 10117 Berlin, Germany.

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September 2016

Evolution of initiator tRNAs and selection of methionine as the initiating amino acid.

RNA Biol 2016 09 20;13(9):810-9. Epub 2016 Jun 20.

a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India.

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September 2016

Is the cellular initiation of translation an exclusive property of the initiator tRNAs?

RNA Biol 2015 ;12(7):675-80

a Department of Microbiology and Cell Biology; Indian Institute of Science ; Bangalore , India.

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March 2016

Use of Mycobacterium smegmatis deficient in ADP-ribosyltransferase as surrogate for Mycobacterium tuberculosis in drug testing and mutation analysis.

PLoS One 2015 13;10(4):e0122076. Epub 2015 Apr 13.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.

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January 2016

Physiological role of FolD (methylenetetrahydrofolate dehydrogenase), FchA (methenyltetrahydrofolate cyclohydrolase) and Fhs (formyltetrahydrofolate synthetase) from Clostridium perfringens in a heterologous model of Escherichia coli.

Microbiology 2016 Jan 3;162(1):145-55. Epub 2015 Nov 3.

2​Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India 1​Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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January 2016

A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily.

Nucleic Acids Res 2015 Sep 24;43(17):8452-63. Epub 2015 Aug 24.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India

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September 2015

Simultaneous presence of fhs and purT genes is disadvantageous for the fitness of Escherichia coli growth.

FEMS Microbiol Lett 2015 Jul 22;362(14). Epub 2015 Jun 22.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India

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July 2015

A genetic analysis of the functional interactions within Mycobacterium tuberculosis single-stranded DNA binding protein.

PLoS One 2014 10;9(4):e94669. Epub 2014 Apr 10.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.

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June 2015

Impact of Mutating the Key Residues of a Bifunctional 5,10-Methylenetetrahydrofolate Dehydrogenase-Cyclohydrolase from Escherichia coli on Its Activities.

Biochemistry 2015 Jun 28;54(22):3504-13. Epub 2015 May 28.

†Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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June 2015

One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia.

J Bacteriol 2015 Feb 1;197(4):717-26. Epub 2014 Dec 1.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India

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February 2015

Paralogous cAMP receptor proteins in Mycobacterium smegmatis show biochemical and functional divergence.

Biochemistry 2014 Dec 1;53(49):7765-76. Epub 2014 Dec 1.

Department of Molecular Reproduction, Development and Genetics and ‡Department of Microbiology and Cell Biology, Indian Institute of Science , Bangalore 560012, India.

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December 2014

An extended Shine-Dalgarno sequence in mRNA functionally bypasses a vital defect in initiator tRNA.

Proc Natl Acad Sci U S A 2014 Oct 22;111(40):E4224-33. Epub 2014 Sep 22.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India

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October 2014

Avoiding acidic region streaking in two-dimensional gel electrophoresis: case study with two bacterial whole cell protein extracts.

J Biosci 2014 Sep;39(4):631-42

Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

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September 2014

How many initiator tRNA genes does Escherichia coli need?

J Bacteriol 2014 Jul 9;196(14):2607-15. Epub 2014 May 9.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India

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July 2014

Hypersensitivity of hypoxia grown Mycobacterium smegmatis to DNA damaging agents: implications of the DNA repair deficiencies in attenuation of mycobacteria.

Mech Ageing Dev 2013 Oct 4;134(10):516-22. Epub 2013 Sep 4.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.

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October 2013

Initiation with elongator tRNAs.

J Bacteriol 2013 Sep 12;195(18):4202-9. Epub 2013 Jul 12.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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September 2013

Role of the ribosomal P-site elements of m²G966, m⁵C967, and the S9 C-terminal tail in maintenance of the reading frame during translational elongation in Escherichia coli.

J Bacteriol 2013 Aug 31;195(16):3524-30. Epub 2013 May 31.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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August 2013

Biochemical properties of MutT2 proteins from Mycobacterium tuberculosis and M. smegmatis and their contrasting antimutator roles in Escherichia coli.

J Bacteriol 2013 Apr 25;195(7):1552-60. Epub 2013 Jan 25.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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April 2013

Mycobacterium tuberculosis MutT1 (Rv2985) and ADPRase (Rv1700) proteins constitute a two-stage mechanism of 8-oxo-dGTP and 8-oxo-GTP detoxification and adenosine to cytidine mutation avoidance.

J Biol Chem 2013 Apr 5;288(16):11252-62. Epub 2013 Mar 5.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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April 2013

Development of a new generation of vectors for gene expression, gene replacement, and protein-protein interaction studies in mycobacteria.

Appl Environ Microbiol 2013 Mar 11;79(5):1718-29. Epub 2013 Jan 11.

National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.

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March 2013

Crowding, molecular volume and plasticity: an assessment involving crystallography, NMR and simulations.

J Biosci 2012 Dec;37(6):953-63

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012.

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December 2012

Unconventional initiator tRNAs sustain Escherichia coli.

Proc Natl Acad Sci U S A 2012 Aug 24;109(32):13058-63. Epub 2012 Jul 24.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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August 2012

Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth.

Mech Ageing Dev 2012 Apr 1;133(4):138-46. Epub 2011 Oct 1.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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April 2012

Chimeras of Escherichia coli and Mycobacterium tuberculosis single-stranded DNA binding proteins: characterization and function in Escherichia coli.

PLoS One 2011 12;6(12):e27216. Epub 2011 Dec 12.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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April 2012

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2012 Feb 21;68(Pt 2):124-8. Epub 2012 Jan 21.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

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February 2012

Base excision and nucleotide excision repair pathways in mycobacteria.

Tuberculosis (Edinb) 2011 Nov 18;91(6):533-43. Epub 2011 Jul 18.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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November 2011

Functional significance of an evolutionarily conserved alanine (GCA) resume codon in tmRNA in Escherichia coli.

J Bacteriol 2011 Jul 20;193(14):3569-76. Epub 2011 May 20.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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July 2011

Uracil excision repair in Mycobacterium tuberculosis cell-free extracts.

Tuberculosis (Edinb) 2011 May 2;91(3):212-8. Epub 2011 Mar 2.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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May 2011

Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNA(fMet) selection on the ribosomal P-site in Escherichia coli.

Nucleic Acids Res 2011 Jan 26;39(1):202-12. Epub 2010 Aug 26.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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January 2011

Detrimental effects of hypoxia-specific expression of uracil DNA glycosylase (Ung) in Mycobacterium smegmatis.

J Bacteriol 2010 Dec 22;192(24):6439-46. Epub 2010 Oct 22.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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December 2010

Recycling of the posttermination complexes of Mycobacterium smegmatis and Escherichia coli ribosomes using heterologous factors.

J Mol Biol 2010 Sep 16;401(5):854-65. Epub 2010 Jun 16.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.

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September 2010

Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2010 Aug 27;66(Pt 8):887-92. Epub 2010 Jul 27.

Molecular Biophysics Unit, Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.

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August 2010

Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli.

Nucleic Acids Res 2010 Apr 7;38(7):2291-301. Epub 2010 Jan 7.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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April 2010

Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis.

Microbiology 2010 Mar 26;156(Pt 3):940-9. Epub 2009 Nov 26.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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March 2010

A distinct physiological role of MutY in mutation prevention in mycobacteria.

Microbiology 2010 Jan 24;156(Pt 1):88-93. Epub 2009 Sep 24.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.

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January 2010

Analysis of the fusA2 locus encoding EFG2 in Mycobacterium smegmatis.

Tuberculosis (Edinb) 2009 Nov;89(6):453-64

Department of Microbiology and Cell Biology, Indian Institute of Science, CNR Rao Circle, Bangalore 560012, India.

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November 2009

Impact of rRNA methylations on ribosome recycling and fidelity of initiation in Escherichia coli.

Mol Microbiol 2009 May;72(3):795-808

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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May 2009

Important role of the nucleotide excision repair pathway in Mycobacterium smegmatis in conferring protection against commonly encountered DNA-damaging agents.

Microbiology 2008 Sep;154(Pt 9):2776-85

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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September 2008

Recycling of ribosomal complexes stalled at the step of elongation in Escherichia coli.

J Mol Biol 2008 Jul 21;380(3):451-64. Epub 2008 May 21.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India.

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July 2008

Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.

Acta Crystallogr D Biol Crystallogr 2008 May 19;64(Pt 5):551-60. Epub 2008 Apr 19.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

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May 2008

Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli.

EMBO J 2008 Mar 21;27(6):840-51. Epub 2008 Feb 21.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India.

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March 2008

A distinct role of formamidopyrimidine DNA glycosylase (MutM) in down-regulation of accumulation of G, C mutations and protection against oxidative stress in mycobacteria.

DNA Repair (Amst) 2007 Dec 16;6(12):1774-85. Epub 2007 Aug 16.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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December 2007

Mutations that alter the regulation of the chb operon of Escherichia coli allow utilization of cellobiose.

Mol Microbiol 2007 Dec 19;66(6):1382-95. Epub 2007 Nov 19.

Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560 012, India.

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December 2007

Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis.

DNA Repair (Amst) 2007 Oct 27;6(10):1517-28. Epub 2007 Jun 27.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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October 2007

Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase.

J Mol Biol 2007 Sep 27;372(1):186-93. Epub 2007 Jun 27.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

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September 2007

Diet-dependent depletion of queuosine in tRNAs in Caenorhabditis elegans does not lead to a developmental block.

J Biosci 2007 Jun;32(4):747-54

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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June 2007

Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2006 Dec 30;62(Pt 12):1231-4. Epub 2006 Nov 30.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

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December 2006

Cloning, expression, purification, crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2006 Sep 26;62(Pt 9):913-5. Epub 2006 Aug 26.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

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September 2006

Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis.

Microbiology 2006 Aug;152(Pt 8):2191-5

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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August 2006

Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3.

J Biosci 2006 Jun;31(2):281-9

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.

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June 2006

Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli.

J Bacteriol 2005 Oct;187(20):6893-901

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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October 2005

Acquisition of a stable mutation in metY allows efficient initiation from an amber codon in Escherichia coli.

Microbiology 2005 Jun;151(Pt 6):1741-50

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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June 2005

A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli.

Nucleic Acids Res 2004 16;32(20):6028-37. Epub 2004 Nov 16.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India.

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December 2004

Mycobacterium tuberculosis and Escherichia coli nucleoside diphosphate kinases lack multifunctional activities to process uracil containing DNA.

DNA Repair (Amst) 2004 Nov;3(11):1483-92

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India.

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November 2004

Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition.

Nucleic Acids Res 2003 Dec;31(24):7216-26

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India.

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December 2003

Complexes of the uracil-DNA glycosylase inhibitor protein, Ugi, with Mycobacterium smegmatis and Mycobacterium tuberculosis uracil-DNA glycosylases.

Microbiology 2003 Jul;149(Pt 7):1647-58

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India.

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July 2003

Common location of determinants in initiator transfer RNAs for initiator-elongator discrimination in bacteria and in eukaryotes.

J Biol Chem 2003 May 13;278(20):17672-9. Epub 2003 Mar 13.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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May 2003

An unexpected absence of queuosine modification in the tRNAs of an Escherichia coli B strain.

Microbiology 2002 Dec;148(Pt 12):3779-87

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.

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December 2002

Analysis of the initiator tRNA genes from a slow- and a fast-growing Mycobacterium.

Arch Microbiol 2002 Oct 24;178(4):288-96. Epub 2002 Jul 24.

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India.

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October 2002

Mutational analysis of the uracil DNA glycosylase inhibitor protein and its interaction with Escherichia coli uracil DNA glycosylase.

J Mol Biol 2002 Aug;321(4):579-90

Department of Microbiology and Cell Biology, Indian Institute of Science, 560 012, Bangalore, India.

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August 2002

Rapid and reliable site-directed mutagenesis using Kunkel's approach.

Methods Mol Biol 2002 ;182:1-6

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.

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May 2002

Structural basis for poor uracil excision from hairpin DNA. An NMR study.

Eur J Biochem 2002 Apr;269(7):1886-94

Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.

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April 2002